To Uncover the Origins of Diseases, Smithsonian Researchers Dust Bat Specimens for Viral Fingerprints

Smithsonian scientists utilize a new formula to extract fragile genetic data from bats collected decades ago

A fruit bat with large, dark eyes, big ears and light brown fur wraps its gray wings around a tree branch.
A greater short-nosed fruit bat climbs a tree in Sri Lanka. Anton Croos, Wikimedia

Over the past 150 years, the National Museum of Natural History has compiled a sprawling collection of more than 147 million specimens and artifacts ranging from whale bones and pinned insects to meteorites and minerals. Thanks to cutting edge research techniques, museum researchers are able to study specimens collected more than a century ago in ways early Smithsonian scientists could not have imagined.

“Museum specimens are a snapshot of the past,” said Kelly Speer, a microbiologist at the museum and a postdoctoral fellow at the Smithsonian Conservation Biology Institute’s Center for Conservation Genomics. For decades, researchers have been using these scientific snapshots to study everything from ancient climate change to the impact of modern environmental issues. 

But an area where museum specimens have been rarely utilized is in the field of emerging diseases. When animal specimens are preserved, traces of the parasites and pathogens infecting them are also preserved. According to Speer, who specializes in studying a suite of parasites that slurp up bat blood, studying these infectious clues would add a “whole new piece of biodiversity that we can understand through museum specimens.”

In recent years, understanding how animals interact with disease has been pushed to the scientific forefront as researchers attempt to trace the rise and spread of COVID-19, an infectious strain of coronavirus. Researchers believe the virus spilled over into humans from bats, who are the reservoir for a variety of other diseases. But pinpointing exactly when and where this coronavirus strain evolved has proven difficult. 

To fill in some of these blanks, Speer and several colleagues at the museum and the National Zoo & Conservation Biology Institute sifted through the museum’s sprawling bat collection, which houses specimens of these frequent fliers from around the world.

After plucking it from its jar, the researchers use tongs to examine a great roundleaf bat from Myanmar. Melissa Hawkins, Smithsonian Institution

In a study published last month in the journal Frontiers in Evolution and Ecology, the researchers examined 22 bat specimens in the museum’s collection that had been collected from Myanmar and China (the vicinity where COVID-19 likely originated) between 1886 and 2003. These bats, which included pug-nosed horseshoe bats and wide-eyed flying foxes, were preserved in a variety of ways. The older specimens were pickled in ethanol while others were fixed in formalin, a chemical concoction that preserves tissues. Some bats were even flash frozen at -320 degrees Fahrenheit using liquid nitrogen. 

To determine if these historic bat specimens possessed any viral traces, the researchers collected lung and small intestine tissue samples from the bats soaking in formalin and ethanol and processed them alongside the flash frozen tissue. They then ran the tissues through a battery of treatments to determine which procedure and preservation method yielded the most RNA. 

Like a chef experimenting with variations of recipes, they eventually calibrated the best steps for extracting genetic material from bats collected decades ago. But the way the bat specimens were prepared played a huge role in whether there were any usable RNA strands left to extract. Flash frozen tissue consistently yielded the highest quality RNA while formalin-fixed and alcohol soaked specimens produced degraded RNA sequences—if they offered anything at all.

The researchers were particularly interested in finding genetic evidence in the form of ribonucleic acid, or RNA, a key molecule responsible for activating, coding and regulating different genes in living cells. Unlike DNA, which is composed of two interwoven strands of proteins, most RNA is single stranded. It also takes on a more active role in our cells. According to Melissa Hawkins, the museum’s curator of mammals who specializes in extracting valuable genetic data from decades-old museum specimens, DNA is often locked away for safekeeping while RNA is out actively coding new proteins and turning different genes on and off. “You have a whole novel in your DNA and genetic code, but the RNA is the excerpts that you need to perform an operation,” said Hawkins, who collaborated with Speer on the new project. “RNA gives you a completely different picture of what’s going on with an animal at a specific point in time”

Several bat specimens in the museum’s mammal collection are preserved in jars of ethanol. In addition to bats, many other small mammals, birds, reptiles, amphibians and fish are stored in similar jars in the museum’s collection. Melissa Hawkins, Smithsonian Institution

When it comes to decoding viruses, uncovering RNA is key. Many viruses, including coronaviruses like COVID-19, store all of their genetic information in RNA. As a result, these insidious infections leave their RNA fingerprints inside their hosts, including bats. 

But dusting for these viral fingerprints is difficult. RNA is much more fragile than DNA and degrades quickly unless it has been carefully collected. And until only recently, few museum specimens were collected with RNA in mind. This makes pinpointing usable strands of RNA as difficult as sifting through a soggy haystack without knowing if a needle is even in there. “Most people don’t think you can go looking for RNA in museum specimens because you just think it would be gone,” said Carly Muletz Wolz, a molecular ecologist who works with Speer at the National Zoo’s Center for Conservation Genomics who was also involved in the new study.

Several of the museum’s tent-making bats, a species native to Central and South America that was not examined in the new study, preserved in a jar of ethanol. Smithsonian Institution

While lugging a flask of liquid nitrogen into the field is a hassle, the difference it makes in preserving high-quality samples was huge according to Hawkins. “Logistically it’s not a lot of fun but it’s clearly very important because it resulted in the highest quality RNA we recovered,” she said. Speer agreed and noted that the quality of the RNA samples they found could be eye-opening. “We showed that you can still get high quality RNA out of flash frozen samples that are 33 years old which I think was surprising,” Speer said.  

The researchers didn’t find any traces of coronaviruses in the 22 bats they examined. But now that they have the steps down and proof that historic RNA can be harnessed from frozen tissue, they are planning to test a much larger batch of bats in the museum’s collection for coronavirus. And these methods can be applied to extract invaluable bits of RNA from a vast array of creatures beyond bats. “It unlocks Smithsonian’s 600,000 mammal specimens for researchers to understand mammalian diversity and pathogen evolution,” Hawkins said.

Screening specimens for viruses can potentially help to flesh out how the pathogens themselves are changing to keep pace with their hosts. This evolutionary arms race also offers insights into how pathogens jump from bats to different hosts, including humans. Untangling where a virus came from and when it spilled into the human world is essential for understanding where it is heading. According to Muletz Wolz, “it is difficult to stop pathogens from emerging when we don’t know where they are coming from.”

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